Ccdc39 coiled-coil domain containing 39 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ccdc39provided by MGI
Official Full Name: coiled-coil domain containing 39provided by MGI
Primary source: MGI:MGI:1289263
See related: Ensembl:ENSMUSG00000027676 AllianceGenome:MGI:1289263
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: prh; D3Ertd789e; b2b1304Clo; b2b1735Clo; b2b2025.1Clo; 4921507O14Rik
Summary: Acts upstream of or within several processes, including cerebrospinal fluid circulation; inner dynein arm assembly; and nervous system development. Located in 9+2 motile cilium; cytosol; and glial cell projection. Is expressed in several structures, including central nervous system; ileum; male reproductive gland or organ; respiratory system; and secondary heart field. Used to study Kartagener syndrome; hydrocephalus; primary ciliary dyskinesia 14; and visceral heterotaxy. Human ortholog(s) of this gene implicated in primary ciliary dyskinesia 14. Orthologous to human CCDC39 (coiled-coil domain 39 molecular ruler complex subunit). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in testis adult (RPKM 10.1), CNS E18 (RPKM 9.6) and 19 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 A3; 3 16.32 cM

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (33864906..33898473, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (33810757..33844325, complement)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Early postnatal microglial ablation in the Ccdc39 mouse model reveals adverse effects on brain development and in neonatal hydrocephalus.
Title: Early postnatal microglial ablation in the Ccdc39 mouse model reveals adverse effects on brain development and in neonatal hydrocephalus.
data provide the first evidence for involvement of Ccdc39 in hydrocephalus and suggest that the proper development of medial wall ependymal cilia is crucial for normal mouse brain development.
Title: A mutation in Ccdc39 causes neonatal hydrocephalus with abnormal motile cilia development in mice.
Ccdc39 is most abundantly expressed in tissues rich in highly ciliated cells, such as olfactory sensory neurons, and is predicted to be important to cilia.
Title: Tissue expression patterns identify mouse cilia genes.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (4) 1 citation
Endonuclease-mediated (2)
Targeted (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BE456625 (e-PCR)
- UniSTS:207479

AI447426 (e-PCR)
- UniSTS:159104

AI844750 (e-PCR)
- UniSTS:178826

NoName (e-PCR)
- UniSTS:234657

D3Ertd789e (e-PCR), detects polymorphism
- UniSTS:167375

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info

Process	Evidence Code	Pubs
involved_in axonemal dynein complex assembly	ISO Inferred from Sequence Orthology more info
involved_in axonemal dynein complex assembly	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within central nervous system myelination	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cerebral cortex development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cerebrospinal fluid circulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cilium movement	ISO Inferred from Sequence Orthology more info
involved_in cilium-dependent cell motility	IBA Inferred from Biological aspect of Ancestor more info
involved_in cilium-dependent cell motility	ISO Inferred from Sequence Orthology more info
involved_in cilium-dependent cell motility	ISS Inferred from Sequence or Structural Similarity more info
involved_in determination of digestive tract left/right asymmetry	IEA Inferred from Electronic Annotation more info
involved_in determination of digestive tract left/right asymmetry	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of liver left/right asymmetry	IEA Inferred from Electronic Annotation more info
involved_in determination of liver left/right asymmetry	ISO Inferred from Sequence Orthology more info
involved_in determination of pancreatic left/right asymmetry	IEA Inferred from Electronic Annotation more info
involved_in determination of pancreatic left/right asymmetry	ISO Inferred from Sequence Orthology more info
involved_in epithelial cilium movement involved in determination of left/right asymmetry	IBA Inferred from Biological aspect of Ancestor more info
involved_in epithelial cilium movement involved in determination of left/right asymmetry	ISO Inferred from Sequence Orthology more info
involved_in epithelial cilium movement involved in determination of left/right asymmetry	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within epithelial cilium movement involved in extracellular fluid movement	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within establishment of left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within establishment of localization in cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in flagellated sperm motility	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within flagellated sperm motility	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart looping	IEA Inferred from Electronic Annotation more info
involved_in heart looping	ISO Inferred from Sequence Orthology more info
involved_in inner dynein arm assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within inner dynein arm assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner dynein arm assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within locomotion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lung development	IEA Inferred from Electronic Annotation more info
involved_in lung development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within microglia differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in motile cilium assembly	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within motile cilium assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuroinflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron maturation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron projection morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein localization to cilium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cilium beat frequency	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cilium beat frequency	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to organic cyclic compound	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within synapse maturation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in 9+2 motile cilium	EXP Inferred from Experiment more info	PubMed
is_active_in axoneme	IBA Inferred from Biological aspect of Ancestor more info
located_in axoneme	ISO Inferred from Sequence Orthology more info
located_in axoneme	ISS Inferred from Sequence or Structural Similarity more info
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in glial cell projection	EXP Inferred from Experiment more info	PubMed

General protein information

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Preferred Names: coiled-coil domain-containing protein 39

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_026222.3 → NP_080498.1 coiled-coil domain-containing protein 39

See identical proteins and their annotated locations for NP_080498.1

Status: VALIDATED

Source sequence(s)

AC154395

Consensus CDS

CCDS17304.1

UniProtKB/Swiss-Prot

B2RSM0, Q8CDG6, Q9D5Y1

Related

ENSMUSP00000029222.6, ENSMUST00000029222.8

Conserved Domains (1) summary

COG1196
Location:22 → 704

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

33864906..33898473 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006535499.5 → XP_006535562.1 coiled-coil domain-containing protein 39 isoform X2

Conserved Domains (1) summary

COG1196
Location:28 → 777

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
XM_006535498.5 → XP_006535561.1 coiled-coil domain-containing protein 39 isoform X1

Conserved Domains (1) summary

COG1196
Location:162 → 801

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
XM_011249686.4 → XP_011247988.1 coiled-coil domain-containing protein 39 isoform X4

Conserved Domains (1) summary

COG1196
Location:86 → 386

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
XM_006535500.5 → XP_006535563.1 coiled-coil domain-containing protein 39 isoform X3

See identical proteins and their annotated locations for XP_006535563.1

Conserved Domains (2) summary

COG1196
Location:306 → 604

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR04523
Location:22 → 622

Mplasa_alph_rch; helix-rich Mycoplasma protein